feat: gitnexus:keep marker preserves custom context sections (resubmit of #605)

gitnexus/src/cli/ai-context.ts

@@ -199,7 +199,9 @@ async function fileExists(filePath: string): Promise<boolean> {
 async function upsertGitNexusSection(
   filePath: string,
   content: string,
-): Promise<'created' | 'updated' | 'appended'> {
+  projectName: string,
+  stats: RepoStats,
+): Promise<'created' | 'updated' | 'appended' | 'preserved'> {
   const exists = await fileExists(filePath);
 
   if (!exists) {
@@ -223,7 +225,50 @@ async function upsertGitNexusSection(
   );
 
   if (startIdx !== -1 && endIdx !== -1 && endIdx > startIdx) {
-    // Replace existing section
+    const existingSection = existingContent.substring(
+      startIdx,
+      endIdx + GITNEXUS_END_MARKER.length,
+    );
+
+    // If the existing section contains <!-- gitnexus:keep -->, preserve the user's
+    // custom layout and only update the stats line (node/edge/flow counts).
+    // This lets teams trim the verbose default template to a lean format without
+    // having it overwritten on every `gitnexus analyze`.
+    //
+    // Note: the keep-marker check operates on `existingSection` (the substring
+    // between valid section markers identified by findSectionMarkerIndex), so
+    // a keep marker in user prose OUTSIDE the GitNexus block has no effect.
+    if (existingSection.includes('<!-- gitnexus:keep -->')) {
+      // Build the new stats line from the caller-provided values directly.
+      // We do NOT re-extract from `content` because:
+      //   (a) first-bold extraction is fragile if the template evolves
+      //   (b) the parenthesized-text fallback can match unrelated tuples
+      //       like `({target: "symbolName", direction: "upstream"})`
+      //       when noStats is set
+      // Passing projectName + stats explicitly makes the contract obvious.
+      // noStats controls template generation, not keep-section stat updates — the user opted into a stats line by keeping it.
+      const newStatsInner = `${stats.nodes || 0} symbols, ${stats.edges || 0} relationships, ${stats.processes || 0} execution flows`;
+      const statsLine = `Indexed as **${projectName}** (${newStatsInner})`;
+
+      // Match either canonical phrasing at line start (`^` with `m` flag) so we
+      // cannot replace prose embedded mid-paragraph. Deliberately no `$`: text
+      // after the closing `)` on the same line (e.g. ". MCP tools.") stays intact.
+      const statsPattern = /^(?:Indexed as|indexed by GitNexus as) \*\*[^*]+\*\* \([^)]+\)/m;
+
+      if (statsPattern.test(existingSection)) {
+        const updatedSection = existingSection.replace(statsPattern, statsLine);
+        const before = existingContent.substring(0, startIdx);
+        const after = existingContent.substring(endIdx + GITNEXUS_END_MARKER.length);
+        await fs.writeFile(filePath, (before + updatedSection + after).trim() + '\n', 'utf-8');
+        return 'updated';
+      }
+      // Keep marker present but no stats line matched. Section is preserved
+      // unchanged on disk; return a distinct status so callers/CLI output
+      // don't mis-report this as 'updated' (which would imply a write).
+      return 'preserved';
+    }
+
+    // No keep marker — replace existing section with full verbose content
     const before = existingContent.substring(0, startIdx);
     const after = existingContent.substring(endIdx + GITNEXUS_END_MARKER.length);
     const newContent = before + content + after;
@@ -344,12 +389,12 @@ export async function generateAIContextFiles(
   if (!options?.skipAgentsMd) {
     // Create AGENTS.md (standard for Cursor, Windsurf, OpenCode, Cline, etc.)
     const agentsPath = path.join(repoPath, 'AGENTS.md');
-    const agentsResult = await upsertGitNexusSection(agentsPath, content);
+    const agentsResult = await upsertGitNexusSection(agentsPath, content, projectName, stats);
     createdFiles.push(`AGENTS.md (${agentsResult})`);
 
     // Create CLAUDE.md (for Claude Code)
     const claudePath = path.join(repoPath, 'CLAUDE.md');
-    const claudeResult = await upsertGitNexusSection(claudePath, content);
+    const claudeResult = await upsertGitNexusSection(claudePath, content, projectName, stats);
     createdFiles.push(`CLAUDE.md (${claudeResult})`);
   } else {
     createdFiles.push('AGENTS.md (skipped via --skip-agents-md)');